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Version 0.1
(original submission)

Basic reporting

The introduction is well written with good examples of complex fetal defects arising from multiple gen aberrations (skeletal malformations and dysplasia). It would be really useful if the authors could provide statistics of genetic aberrations associated with fetal malformations. For example, how many of the fetal malformation syndromes are associated with a single gene? How many are due to multiple genetic defects in groups of genes/pathways? What are the challenges associated with variant prioritization in these complex cases?

Experimental design

The number of samples selected, although small does cover a broad range of fetal defects. More information on the selection of genes would be of tremendous value. A paragraph on the manual curation of the genes would help others in the field to weigh variants in genes associated with other phenotypes. Also, more details on the Fetalis EMA algorithm are needed:
1) The type of algorithm - is it a classification one or based on weighting of the variants in a select few genes.
2) Which variables (population frequency, SIFT scores, nonsense mutation, etc) are key to the weighting of the variants in a gene?

Validity of the findings

The findings are impressive with not a single mis-diagnosis made. If more details on the algorithm are provided, the tool would have great potential to be used routinely.

Basic reporting

The manuscript entitled, "First applications..." by Pangalos et al, reports the first diagnostic application of a new targeted exome sequencing strategy for fetuses detected with ultrasound abnormalities.

The results provide without ambiguity the usefulness of this approach with a greater diagnostic value. The small sample size used in the investigation warrants for inclusion of more number of cases to evaluate the approach. However, the current work provides a proof of principle of this novel diagnostic strategy with a potential for greater sensitivity/specificity than the existing methods.

The manuscript is overall written well to appropriately report the results of the investigation. Minor style correction: The headings in the abstract (Background, Methods.. etc), should be bold followed by a period and begin with a new paragraph.

Experimental design

The authors can elaborate a little on the core algorithm in Fetalis & EMA pipeline.

Line 176: The authors can attempt to clarify the variant prioritization algorithm, which is stated to be based on 3 Ultrasonographic (US)findings , and filtering functions in EMA pipeline. How are variants selected based on US findings? Do the authors use previous literature annotations for variants for the specific US findings?

Validity of the findings

This results reflect a good design, resulting in good read coverage required for the variant analysis. The authors provided the details of sequencing such as raw reads, coverage as a supplementary table. They also used the default parameters of the software for analysis of raw data, variant calling and annotation. However, the unique aspects of their approach is the use of the Fetalis list of genes and the variant prioritization method. It is felt that the results of variant prioritization are not sufficiently provided.
Not absolutely essential, but the authors may report a table reflecting the process of shortlisting of the variants for each case. It could include the total number of all identified variants, the variants through the hierarchical selection process (low importance, high importance and finally reported variants ) for each case. A supplementary table with this information would add value to the elucidation of the Fetalis-EMA algorithm.

phrase clarification :
line 207: On average, a total of approximately 2200+/- 50 .........
From the context it is clear that the authors are providing the number of genomic features in which the variants occur. In that case, "~1030 exonic" might mislead into giving a meaning "1030 variants are exonic" (meaning 1030 variants occur in exons). The correct phrase could be, "~1030 exons" (meaning occur in 1030 exons).
This needs to be clarified.

The authors overall provided a straight forward interpretation of the results, with little or no speculation and discusses well the advantages as well as the limitations of their approach. They discuss well the significance of the current Fetalis-EMA approach in terms of its timely availability of results, cost effectiveness, lower ethical concerns such as avoidance of unnecessary incidental findings and , especially in the borderline cases where the Ultrasound findings doesn't clearly provide a definitive risk assessment.

The negative results in some of the Fetalis-EMA cases turn out to be true negatives, that essentially improves the specificity of the algorithm.

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